Structural differences between ribosomes of various eukaryotes: stability, density, mass, size and structure in solution of cytoplasmic ribosomes from Tetrahumena, Artemia and Euglena

Cytoplasmic ribosomal particles were isolated from the ciliated protozoa Tetrahymena pyriformis, the brine shrimp Artemia, and the flagellated alga Euglena gracilis; their stability, density, mass, size and structure in solution have been compared in identical conditions. The small and in particular the large subunits of Euglena ribosomes were less stable than the corresponding particles of the other eukaryotes. Equilibrium centrifugation of the ribosomes of the various species in CsCl density gradients revealed no difference in either their homogeneity or their buoyant density; so no differences were detected in this way in the ratio of their RNA to protein content or in their partial specific volume. Using analytical boundary sedimentation, the sedimentation coefficients s_20,w⁰ of the whole ribosomes were measured to be 81, 81 and 86 S, respectively. Photon correlation spectroscopy of laser light scattered by the whole ribosomes has yielded values for their diffusion coeffcient D_20,w⁰) of 1.51, 1.42 and 1.29 × 10⁻⁷ cm² s⁻¹, respectively; this corresponds to values for their hydrodynamic radius of 142, 151 and 166 Å, respectively. The data indicate also that the solvation of the ribosomes increases with their size and mass.So evidence has been obtained for differences in the size of various eukaryotic ribosomes, and even in the degree of compactness of their structure in solution.     

Visualization of cytosolic ribosomes on the surface of mitochondria by electron cryo‐tomography

We employed electron cryo‐tomography to visualize cytosolic ribosomes on the surface of mitochondria. Translation‐arrested ribosomes reveal the clustered organization of the TOM complex, corroborating earlier reports of localized translation. Ribosomes are shown to interact specifically with the TOM complex, and nascent chain binding is crucial for ribosome recruitment and stabilization. Ribosomes are bound to the membrane in discrete clusters, often in the vicinity of the crista junctions. This interaction highlights how protein synthesis may be coupled with transport. Our work provides unique insights into the spatial organization of cytosolic ribosomes on mitochondria.     

Reassociation of cytoplasmic ribosomal subunits of barley and its virescens mutant to form active hybrids

Polyphenylalamine synthesis by cytoplasmic ribosomes of Gateway barley (Hordeum vulgare) and its virescens single gene nuclear mutant was compared. The cytoplasmic 80S ribosomes were isolated from unimbibed embryo material and the ribosomes were dissociated into their component 60S and 40S subunits by centrifugation through sucrose gradients containing high KCl-to-MgCl₂ buffer. These separated subunits could be reassociated by resuspension in buffer having about equimolar concentrations of MgCl₂ and KCl. Both homologous and heterologous combinations of the subunits reassociated to give monomeric 80S ribosomes, and the derived monomers as well as various combinations of the individual subunits showed equivalent activity in an in vitro system for poly (U)-directed polyphenylalanine synthesis.     

Mitochondrial ribosomes in a trypanosome

The nature, and even the existence, of trypanosome mitochondrial ribosomes has been the subject of some debate. We investigated this further in the insect trypanosome, Crithidia fasciculata. In sucrose gradients of parasite lysates, mitochondrial ribosomal RNA co-sediments at approximately 35S with nascent peptides synthesized in the presence of the cytosolic translational inhibitor, cycloheximide. Co-sedimenting peptides in this peak are much reduced when the parasites are treated with the bacterial translational inhibitor, chloramphenicol. In CsCl gradients this peak resolves at a buoyant density of 1.42 g/cm(3), a value typical for mito-ribosomes. Electron microscopy of peak material shows particles smaller than cytosolic ribosomes, but with characteristic ribosomal shapes. We propose that these particles represent the parasite's mitochondrial ribosomes.     

Protein Electrophoretic Analysis of Amyloplast and Cytoplasm Ribosomes from Lotus Cotyledon

Amyloplasts and cytoplasmic ribosomes in cotyledon cells of lotus (Nelvmbo nucifeva Gaertn. ) have been observed on the basis of morphology. Isolation of these ribosomes by centrifugation through 30% to 55% (W/V) sucrose density gradient resulted in three bands of amyloplasts ribosomes and four bands of cytoplasmic ribosomes. The authors used these ribosomes bands for SDS-PAGE electrophoresis to analyse ribosomes of proteins. The patterns of SDS-PAGE between cytoplasmic ribosomes of proteins and amyloplasts ribosomes of proteins were different. The amyloplasts ribosomes of proteins showed 26 kD and 23 kD bands, and the cytoplasmic ribosomes of proteins showed 65 kD band. The analysis of electrophoretic patterns of the cytoplasmic ribosomes of proteins showed that there was a newly synthesized ribosomes protein with 19 kD molecular weight in 18 to 20 days after fertilization.     

Analysis of the secondary structure of expansion segment 39 in ribosomes from fungi, plants and mammals

The structure of expansion segment 39, ES39, in eukaryotic 23 S-like ribosomal RNA was analysed using a combination of chemical and enzymic reagents. Ribosomes were isolated from yeast, wheat, mouse, rat and rabbit, five organisms representing three different eukaryotic kingdoms. The isolated ribosomes were treated with structure-sensitive chemical and enzymic reagents and the modification patterns analysed by primer extension and gel electrophoresis on an ABI 377 automated DNA sequencer. The expansion segment was relatively accessible to modification by both enzymic and chemical probes, suggesting that ES39 was exposed on the surface of the ribosomes. The collected modification data were used in secondary structure modelling of the expansion segment. Despite considerable variation in both sequence and length between organisms from different kingdoms, the structure analysis of the expansion segment gave rise to structural fingerprints that allowed identification of homologous structures in ES39 from fungi, plants and mammals. The homologous structures formed an initial helix and an invariant hairpin connected to the initial helix via a long single-stranded loop. The remaining part of the ES39 sequences accounted for most of the length variation seen between the analysed species. This part could form additional, albeit less similar, hairpins. A comparison of ES39 sequences from other fungi, plants and mammals showed that identical structures could be formed in these organisms.     

Ribosomes of Brachionus plicatilis (Rotifera) – distribution in homogenate fractions and general properties

(1) The content of DNA, RNA and of proteins of Brachionus plicatilis was estimated and the distribution of RNA and of proteins of different homogenate fractions characterised. (2) Ribosomes were isolated from Brachionus plicatilis homogenates and were characterised by gradient centrifugation. (3) Unlike the RNA content, the yield of ribosomes from different homogenate fractions is strongly dependent on the concentration of Mg²⁺-ions in the buffers. Likewise resuspension of ribosomes is more effective in Mg²⁺- (or Ca²⁺-) free buffers. (4) Dissociation of ribosomes was brought about by centrifugation of ribosomes in gradients containing less than 4 mM Mg²⁺. In this case, beside the peaks of subunits, a peak in the region of 80 S remained which vanished only under conditions destroying ribosomal material altogether. (5) Proteins were isolated from ribosomal subunits and from undissociated ribosomes and were characterised by two-dimensional gel electrophoresis techniques. Patterns of 51 spots were regularly obtained from large subunits and patterns of 41 spots from small subunits. The undissociated ribosomes showed 83 spots, most of which could be attributed to the large or the small subunit. The ribosomal proteins have molecular masses of between 11000 and 56000 Da, while the molecular mass of the total protein content of Brachionus ribosomes was estimated to be 1.8 ±0.5) ×10⁶ Da.     

Evolution of proteins in mammalian cytoplasmic and mitochondrial ribosomes

Summary The proteins of cytoplasmic and mitochondrial ribosomes from the cow and the rat were analyzed by co-electrophoresis in two dimensional polyacrylamide gels to determine their relative evolutionary rates. In a pairwise comparison of individual ribosomal proteins (r-proteins) from the cow and the rat, over 85% of the cytoplasmic r-proteins have conserved electrophoretic properties in this system, while only 15% of the proteins of mitochondrial ribosomes from these animals fell into this category. These values predict that mammalian mitochondrial r-proteins are evolving about 13 times more rapidly than cytoplasmic r-proteins. Based on actual evolutionary rates for representative cytoplasmic r-proteins, this mitochondrial r-protein evolutionary rate corresponds to an amino acid substitution rate of 40×10^–10 per site per year, placing mitochondrial r-proteins in the category of rapidly evolving proteins. The mitochondrial r-proteins are apparently evolving at a rate comparable to that of the mitochondrial rRNA, suggesting that functional constraints act more or less equally on both kinds of molecules in the ribosome. It is significant that mammalian mitochondrial r-proteins are evolving more rapidly than cytoplasmic r-proteins in the same cell, since both sets of r-proteins are encoded by nuclear genes. Such a difference in evolutionary rates implies that the functional constraints operating on ribosomes are somewhat relaxed for mitochondrial ribosomes.Presented at the FEBS Symposium on Genome Organization and Evolution, held in Crete, Greece, September 1–5, 1986     

Phytochrome controlled acid RNase: An “attached” protein of ribosomes

The light-dependent increment in RNase activity (which is ribosome bound in cell extracts) is distributed as a gradient increasing from base to hook of lupin hypocotyls. No evidence was found of non-specific or of specific activation of pre-formed enzyme molecules following isolation, either before or after (latent activity) destruction of particles. The autodegradation capacity of ribosomes isolated from irradiated cells was almost double that of ribosomes from etiolated tissue. It is proposed that association between the bulk of the light-controlled RNase fraction and lupin ribosomes results from binding of soluble protein. It is not clear whether binding is specific or an artifact of isolation.     

Kinetic and thermodynamic studies of peptidyltransferase in ribosomes from the extreme thermophile Thermus thermophilus

Throughout evolution, emerging organisms survived by adapting existing biochemical processes to new reaction conditions. Simple protein enzymes balanced changes in structural stability with changes that permitted optimal catalysis by adjustments in both entropic and enthalpic contributions to the free energy of activation for the reaction. Study of adaptive mechanisms by large multicomponent enzymes such as the ribosome has been largely unexplored. Here we have determined the kinetic and thermodynamic parameters of peptidyltransferase in ribosomes from the extreme thermophile Thermus thermophilus. Activity of thermophilic enzymes can be assayed over a wide range of temperatures, enabling one to measure accurate catalytic rates and determine enthalpic and entropic contributions to the free energy of activation of the reaction. Differences in the reaction conditions used here and in published studies on mesophilic ribosomes prevent direct comparison, but our data on Thermus ribosomes suggest that these ribosomes have adapted to changing environments using the same strategies as simple protein enzymes, balancing stability and flexibility without loss of catalytic rate. This strategy must be a very ancient process, perhaps first used by primitive ribosomes in the RNA World.     

Protein Synthesis by a Cell-Free Preparation from the Bird Malaria,Plasmodium lophurae*

SYNOPSIS. Cytoplasmic polyribosomes were isolated from the avian malaria parasite Plasmodium lophurae by lysis with 0.15% Triton X-100 followed by high speed centrifugation through a discontinuous sucrose gradient. Polyribosomes were protected from nuclease degradation using 100 μg/ml heparin or 50 μg/ml dextran sulfate. Cell-free incorporation of radioisotope-labeled amino acids required a pH 5 fraction (duck reticulocyte), Mg²⁺, and an energy-generating system. The protein synthesizing system was stimulated by the addition of polyuridylic acid. Optimum conditions for protein synthesis by the plasmodial system are described. The effects of drugs on the cell-free protein synthesizing system using duck reticulocyte and plasmodial ribosomes are reported.     

Induction of candidicidal activity in mice by immunization with Candida albicans ribosomes

Abstract Mice immunized with ribosomes from Candida albicans are protected against experimental systemic candidiasis. In this study we investigated the candidacidal activity of spleen cells from immunized animals as measured by ⁵¹Cr release from pre-labelled yeast cells. It was found that the anti-candidal cytotoxic activity of splenocytes from immunized mice was significantly higher than that of spleen cells from non-immunized controls with various effector to target (E:T) ratios, but optimal results were obtained with an E:T ratio of 10:1. The cytotoxic activity of splenocytes as measured by the ⁵¹Cr release assay correlated well with the capacity of the cells to inhibit candidal growth as determined by quantitative plating. This candidacidal activity was not antibody dependent but increased killing was obtained by adding fresh (but not heat inactivated) mouse serum. The enhanced candidicidal activity was inhibited by removal of plastic- or nylon-adherent cells from the cell suspension but not by treatment with anti-Thy 1.2 serum and complement. The data indicate that a candidacidal cell population is induced in the spleens of animals immunized with C. albicans ribosomes.     

Dependence of the quality and the in vitro translation capacity of pine ribosome assemblies on the isolation procedure

The in vitro translation capacity of total ribosome assemblies isolated from the vegetative buds of small Scots pine (Pinus sylvestris L.) plants depends on the isolation procedure. Good yields and high values for protein synthesis were obtained in experiments in which polyvinyl pyrrolidone (PVP) was added to the grinding buffer. The polysome profiles obtained after sucrose density gradient centrifugation indicated the presence of polysomes in all samples. In addition, large ribosome aggregates were visible in the scanning electron micrographs. The use of an RNase inhibitor (RNasin) together with PVP did not improve the results, and treatment with ribonuclease (RNase, EC 3.1.27.5) destroyed the ability to synthesize protein. D, L-Dithiothreitol (DTT) and mercaptoethanol, if used instead of or together with PVP, gave low yields and also DTT destroyed the in vitro translation capacity of the ribosome assemblies. The polysome profiles had a high peak indicating dimers and often a descending series of peaks indicating polymers. A study of the scanning electron micrographs gave the impression that the largest polymers and aggregates had broken down. Protease K (EC 3.4.21.14) when added to the grinding buffer also destroyed the ability of the ribosomes to maintain protein synthesis in vitro. In this case, the shape of the polysome profiles gave the impression of successful isolation. Clumps of ribosomes, presumably originating from large aggregates, were visible in the scanning electron micrographs. Triton X-100 and 0.25 M NaCl in the grinding buffer extracted chromatin, which affected the results. The material lost during the extraction and purification processes consisted mainly of monosomes and their sub-units. On the basis of the above results it was concluded that the preservation of large polysomes and ribosome aggregates in the isolated ribosome assemblies is necessary if they are to maintain a high translation capacity. The content of the assemblies was best revealed in the scanning electron micrographs. The shape of the polysome profiles did not always correlate with the ability of the isolated ribosomes to synthesize proteins.     

Effect of High Temperature on Chloroplast Ribosomes and Biosynthesis of Chloroplast Proteins in Wheat

The chloroplasts of wheat have chanced greatly at high temperature condition(34℃). When wheat grown at 34℃ for 10 days, its chlorophyll content was 6 times less than that under the normal condition(22℃). The ribosomes were isolated from the leaves by sucrose density gradient centrifugation. It is found that only 80 S ribosomes existed in wheat leaves grown at the high temperature and the formation of 70 S ribosomes is specifically prevented. Since the absence of 70 S ribosomes in chloroplast, proteins synthesis can no longer proceed. Analysis of SDS-polyacrylamide gel electrophoresis indicates that the bands of chloroplast proteins from the leaves of wheat at the high temperature are less than those under normal condition. One of the poly- peptides the large subunit(MW=57000 daltons) of ribulose bisphosphate carboxylase, which is coded for by chloroplast genome and synthesized on 70 S ribosome in chloroplast, was lost. The photosynthetic intensity is decreased due to the blocking synthesis in chloroplast of some polypeptides which play the important role in photosynthesis.     

The Ribosomes of the Simian Malaria,Plasmodium knowlesi. I. Isolation and Characterization*

SYNOPSIS. Monomeric ribosomes, isolated from the monkey malaria Plasmodium knowlesi by the combined use of low concentrations of Triton X-100 and differential centrifugation, sedimented in the SOS range and could be dissociated into 60 and 40S subparticles. The base composition of the rRNA was typically protozoan; that is, low in guanine and cytosine residues.     

Pokeweed antiviral protein inactivates pokeweed ribosomes; implications for the antiviral mechanism

Pokeweed antiviral protein (PAP) and other ribosome-inactivating proteins (RIPs) had previously been thought to be incapable of attacking conspecific ribosomes, thus having no effect on endogenous processes. This assertion conflicts with a model for PAP's in vivo antiviral mechanism in which PAP (a cell wall protein) selectively enters virus-infected cells and disrupts protein synthesis, thus causing local suicide and preventing virus replication. We show here that pokeweed ( Phytolacca americana ) ribosomes, as well as endod ( Phytolacca dodecandra ) ribosomes, are indeed highly sensitive to inactivation by conspecific RIPs. Ribosomes isolated from RIP-free pokeweed and endod suspension culture cells were found to be highly active in vitro , as measured by poly(U)-directed polyphenylalanine synthesis. Phytolacca ribosomes challenged with conspecific RIPs generated doseresponse curves (IC₅₀ of 1 nM PAP or dodecandrin) very similar to those from wheat germ ribosomes. To determine if Phytolacca cells produce a cytosolic 'anti-RIP' protective element, ribosomes were combined with Phytolacca postribosomal supernatant factors from culture cells, then challenged with conspecific RIPs. Resulting IC₅₀ values of 3–7 nM PAP, PAP-II, PAP-S or dodecandrin indicate that supernatants from these Phytolacca cells lack a ribosomal protective element. This research demonstrates that PAP inactivates pokeweed ribosomes (and is therefore potentially toxic to pokeweed cells) and supports the local suicide model for PAP's in vivo antiviral mechanism. The importance of spatial separation between PAP and ribosomes of cells producing this RIP is emphasized, particularly if crop plants are transformed with the PAP gene to confer antiviral protection.     

Membrane binding of ribosomes occurs at SecYE-based sites in the Archaea Haloferax volcanii

Whereas ribosomes bind to membranes at eukaryal Sec61alphabetagamma and bacterial SecYEG sites, ribosomal membrane binding has yet to be studied in Archaea. Accordingly, functional ribosomes and inverted membrane vesicles were prepared from the halophilic archaea Haloferax volcanii. The ability of the ribosomes to bind to the membranes was determined using a flotation approach. Proteolytic pretreatment of the vesicles, as well as quantitative analyses, revealed the existence of a proteinaceous ribosome receptor, with the affinity of binding being comparable to that found in Eukarya and Bacteria. Inverted membrane vesicles prepared from cells expressing chimeras of SecE or SecY fused to a cytoplasmically oriented cellulose-binding domain displayed reduced ribosome binding due to steric hindrance. Pretreatment with cellulose drastically reduced ribosome binding to chimera-containing but not wild-type vesicles. Thus, as in Eukarya and Bacteria, ribosome binding in Archaea occurs at Sec-based sites. However, unlike the situation in the other domains of Life, ribosome binding in haloarchaea requires molar concentrations of salt. Structural information on ribosome-Sec complexes may provide insight into this high salt-dependent binding.